HEADER DNA 06-JAN-04 1S1K TITLE INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*(1AP)P*GP*TP*AP*CP*TP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, DOUBLE HELIX, 2, 6-DIAMINOPURINE, MINOR GROOVE INTERACTIONS, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.A.HAYS,J.WATSON,P.S.HO REVDAT 3 23-AUG-23 1S1K 1 REMARK LINK ATOM REVDAT 2 24-FEB-09 1S1K 1 VERSN REVDAT 1 31-AUG-04 1S1K 0 JRNL AUTH F.A.HAYS,Z.J.JONES,P.S.HO JRNL TITL INFLUENCE OF MINOR GROOVE SUBSTITUENTS ON THE STRUCTURE OF JRNL TITL 2 DNA HOLLIDAY JUNCTIONS. JRNL REF BIOCHEMISTRY V. 43 9813 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15274635 JRNL DOI 10.1021/BI049461D REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : CNS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 29235.770 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 2413 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 228 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.017 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 287 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 34 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.069 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 203 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.22000 REMARK 3 B22 (A**2) : 3.22000 REMARK 3 B33 (A**2) : -6.45000 REMARK 3 B12 (A**2) : 3.51000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.067 REMARK 3 BOND ANGLES (DEGREES) : 6.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 5.460 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 103.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2528 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 17.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1P4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5MM TRIS(HCL), 23MM CAACETATE, 16% REMARK 280 MPD, .6MM DNA AGAINST 28% MPD AT RT, PH 7.50, VAPOR DIFFUSION, REMARK 280 SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.51867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.03733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.27800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.79667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.75933 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.51867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 59.03733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.79667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 44.27800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 14.75933 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE FULL BIOLOGICAL UNIT REMARK 300 CONSISTS OF TWO STRANDS FORMING A B-DNA DUPLEX STRUCTURE. REMARK 300 SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL REMARK 300 MOLECULE(S). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 0.866025 0.000000 16.47850 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -28.54160 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 14.75933 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 11 LIES ON A SPECIAL POSITION. REMARK 375 CA CA A 14 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 32 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O4' DC A 2 O HOH A 48 2.03 REMARK 500 OP2 DA A 6 O HOH A 37 2.04 REMARK 500 O2 DT A 5 O HOH A 49 2.10 REMARK 500 OP1 DG A 9 O HOH A 16 2.11 REMARK 500 O HOH A 35 O HOH A 41 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 37 O HOH A 37 8555 1.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A 1 C3' DC A 1 C2' -0.053 REMARK 500 DC A 1 C2' DC A 1 C1' 0.087 REMARK 500 DC A 1 C4 DC A 1 C5 0.053 REMARK 500 DC A 1 C5 DC A 1 C6 0.125 REMARK 500 DC A 2 P DC A 2 OP2 0.115 REMARK 500 DC A 2 C3' DC A 2 C2' -0.048 REMARK 500 DC A 2 C4 DC A 2 N4 0.106 REMARK 500 DC A 2 N1 DC A 2 C2 0.083 REMARK 500 DC A 2 C5 DC A 2 C6 -0.051 REMARK 500 DG A 4 P DG A 4 O5' 0.070 REMARK 500 DG A 4 O3' DG A 4 C3' -0.121 REMARK 500 DG A 4 C2 DG A 4 N3 0.059 REMARK 500 DG A 4 C4 DG A 4 C5 -0.083 REMARK 500 DG A 4 C8 DG A 4 N9 -0.095 REMARK 500 DG A 4 O3' DT A 5 P -0.081 REMARK 500 DT A 5 C2' DT A 5 C1' 0.115 REMARK 500 DT A 5 O3' DT A 5 C3' -0.164 REMARK 500 DT A 5 C1' DT A 5 N1 0.106 REMARK 500 DT A 5 C2 DT A 5 N3 -0.077 REMARK 500 DT A 5 C4 DT A 5 C5 -0.102 REMARK 500 DT A 5 C6 DT A 5 N1 0.051 REMARK 500 DT A 5 C2 DT A 5 O2 0.090 REMARK 500 DT A 5 C4 DT A 5 O4 -0.074 REMARK 500 DT A 5 C5 DT A 5 C7 -0.043 REMARK 500 DA A 6 P DA A 6 OP1 -0.199 REMARK 500 DA A 6 P DA A 6 OP2 0.135 REMARK 500 DA A 6 P DA A 6 O5' -0.061 REMARK 500 DA A 6 C2 DA A 6 N3 -0.080 REMARK 500 DA A 6 N3 DA A 6 C4 -0.038 REMARK 500 DA A 6 C5 DA A 6 C6 0.124 REMARK 500 DA A 6 C6 DA A 6 N6 -0.162 REMARK 500 DC A 7 P DC A 7 O5' -0.109 REMARK 500 DC A 7 C2 DC A 7 O2 -0.060 REMARK 500 DC A 7 C4 DC A 7 N4 -0.088 REMARK 500 DC A 7 N1 DC A 7 C6 -0.073 REMARK 500 DC A 7 O3' DT A 8 P 0.132 REMARK 500 DT A 8 P DT A 8 OP2 0.176 REMARK 500 DT A 8 C2' DT A 8 C1' -0.110 REMARK 500 DT A 8 O4' DT A 8 C4' -0.115 REMARK 500 DT A 8 O3' DT A 8 C3' -0.040 REMARK 500 DT A 8 C5 DT A 8 C6 -0.079 REMARK 500 DT A 8 C2 DT A 8 O2 -0.119 REMARK 500 DT A 8 C5 DT A 8 C7 -0.092 REMARK 500 DG A 9 P DG A 9 OP1 -0.128 REMARK 500 DG A 9 P DG A 9 OP2 -0.143 REMARK 500 DG A 9 C2 DG A 9 N3 0.091 REMARK 500 DG A 9 N3 DG A 9 C4 -0.068 REMARK 500 DG A 9 C6 DG A 9 N1 -0.056 REMARK 500 DG A 9 C2 DG A 9 N2 0.149 REMARK 500 DG A 9 C6 DG A 9 O6 -0.091 REMARK 500 REMARK 500 THIS ENTRY HAS 59 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 1 N1 - C2 - N3 ANGL. DEV. = 5.6 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 2 O3' - P - OP2 ANGL. DEV. = 15.4 DEGREES REMARK 500 DC A 2 O5' - P - OP2 ANGL. DEV. = -8.3 DEGREES REMARK 500 DC A 2 C5' - C4' - C3' ANGL. DEV. = -11.8 DEGREES REMARK 500 DC A 2 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 DG A 4 O3' - P - OP2 ANGL. DEV. = 26.4 DEGREES REMARK 500 DG A 4 O3' - P - OP1 ANGL. DEV. = -28.7 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A 4 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 4 C4 - C5 - N7 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 4 C5 - N7 - C8 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT A 5 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 5 C2' - C3' - O3' ANGL. DEV. = -26.8 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA A 6 O3' - P - OP1 ANGL. DEV. = -14.9 DEGREES REMARK 500 DA A 6 O5' - P - OP1 ANGL. DEV. = -7.4 DEGREES REMARK 500 DA A 6 O5' - P - OP2 ANGL. DEV. = 11.5 DEGREES REMARK 500 DA A 6 C1' - O4' - C4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DA A 6 C6 - N1 - C2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA A 6 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 7 O3' - P - OP2 ANGL. DEV. = 13.6 DEGREES REMARK 500 DC A 7 O3' - P - OP1 ANGL. DEV. = -26.9 DEGREES REMARK 500 DC A 7 O5' - P - OP1 ANGL. DEV. = 18.6 DEGREES REMARK 500 DC A 7 O5' - P - OP2 ANGL. DEV. = -7.4 DEGREES REMARK 500 DC A 7 C5' - C4' - O4' ANGL. DEV. = -22.6 DEGREES REMARK 500 DC A 7 C2 - N3 - C4 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT A 8 C1' - O4' - C4' ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 9 O3' - P - O5' ANGL. DEV. = 19.2 DEGREES REMARK 500 DG A 9 O3' - P - OP2 ANGL. DEV. = 13.0 DEGREES REMARK 500 DG A 9 O3' - P - OP1 ANGL. DEV. = -22.1 DEGREES REMARK 500 DG A 9 O5' - P - OP2 ANGL. DEV. = -8.6 DEGREES REMARK 500 DG A 9 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 9 C5' - C4' - O4' ANGL. DEV. = -12.4 DEGREES REMARK 500 DG A 9 C3' - C2' - C1' ANGL. DEV. = -8.2 DEGREES REMARK 500 DG A 9 O4' - C1' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 DG A 9 C6 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 10 O3' - P - O5' ANGL. DEV. = 14.0 DEGREES REMARK 500 DG A 10 O5' - P - OP1 ANGL. DEV. = -14.1 DEGREES REMARK 500 DG A 10 C5' - C4' - O4' ANGL. DEV. = 12.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 55 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA A 6 0.09 SIDE CHAIN REMARK 500 DC A 7 0.13 SIDE CHAIN REMARK 500 DG A 9 0.08 SIDE CHAIN REMARK 500 DG A 10 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 15 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 5 OP1 REMARK 620 2 HOH A 31 O 101.0 REMARK 620 3 HOH A 36 O 57.7 145.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 14 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 7 OP2 REMARK 620 2 DC A 7 OP2 169.6 REMARK 620 3 HOH A 23 O 105.6 72.0 REMARK 620 4 HOH A 28 O 81.5 104.3 159.0 REMARK 620 5 HOH A 28 O 102.5 84.2 52.3 107.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 11 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 20 O REMARK 620 2 HOH A 20 O 107.8 REMARK 620 3 HOH A 45 O 125.9 107.2 REMARK 620 4 HOH A 45 O 107.6 124.7 83.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 15 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P4Z RELATED DB: PDB REMARK 900 UNMODIFIED ACT STRAND DBREF 1S1K A 1 10 PDB 1S1K 1S1K 1 10 SEQRES 1 A 10 DC DC 1AP DG DT DA DC DT DG DG MODRES 1S1K 1AP A 3 DA 2,6-DIAMINOPURINE NUCLEOTIDE HET 1AP A 3 22 HET CA A 11 1 HET CA A 14 1 HET NA A 15 1 HETNAM 1AP 2,6-DIAMINOPURINE NUCLEOTIDE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 1 1AP C10 H15 N6 O6 P FORMUL 2 CA 2(CA 2+) FORMUL 4 NA NA 1+ FORMUL 5 HOH *40(H2 O) LINK O3' DC A 2 P 1AP A 3 1555 1555 1.63 LINK O3' 1AP A 3 P DG A 4 1555 1555 1.63 LINK O3' 1AP A 3 OP1 DG A 4 1555 1555 1.94 LINK OP1 DT A 5 NA NA A 15 1555 1555 2.50 LINK OP2 DC A 7 CA CA A 14 1555 1555 2.54 LINK OP2 DC A 7 CA CA A 14 8555 1555 2.45 LINK CA CA A 11 O HOH A 20 1555 1555 3.15 LINK CA CA A 11 O HOH A 20 1555 8555 3.17 LINK CA CA A 11 O HOH A 45 1555 1555 2.83 LINK CA CA A 11 O HOH A 45 1555 8555 2.84 LINK CA CA A 14 O HOH A 23 1555 8555 3.36 LINK CA CA A 14 O HOH A 28 1555 1555 2.38 LINK CA CA A 14 O HOH A 28 1555 8555 2.34 LINK NA NA A 15 O HOH A 31 1555 1555 1.80 LINK NA NA A 15 O HOH A 36 1555 1555 2.73 SITE 1 AC1 1 HOH A 45 SITE 1 AC2 2 DC A 7 HOH A 28 SITE 1 AC3 3 DT A 5 HOH A 31 HOH A 36 CRYST1 32.957 32.957 88.556 90.00 90.00 120.00 P 61 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030343 0.017518 0.000000 0.00000 SCALE2 0.000000 0.035037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011292 0.00000